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Porcine single nucleotide polymorphisms and their functional effect: an update.

B N Keel1, D J Nonneman2, A K Lindholm-Perry2

  • 1USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA. brittney.keel@ars.usda.gov.

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Summary
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Researchers identified over 26 million single nucleotide polymorphisms (SNP) in the swine genome, significantly expanding the catalog of functional genetic variants for pigs. This comprehensive SNP dataset aids future genetic studies and breeding advancements.

Keywords:
Functional variationGenome sequenceLoss-of-functionSwine

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Area of Science:

  • Genomics
  • Animal Genetics
  • Bioinformatics

Background:

  • Accurate identification of genetic variants is crucial for understanding swine genome function and improving breeding programs.
  • Previous studies have identified single nucleotide polymorphisms (SNP) in the swine genome, but a comprehensive catalog is still developing.

Purpose of the Study:

  • To expand the comprehensive list of functional variants in the swine genome by identifying single nucleotide polymorphisms (SNP).
  • To leverage whole genome sequencing data from an increased number of pigs and the updated Sscrofa 11.1 reference genome.

Main Methods:

  • Whole genome sequencing of 240 pigs.
  • Identification and classification of high-confidence single nucleotide polymorphisms (SNP).
  • Utilizing the Sscrofa 11.1 reference genome for variant calling.

Main Results:

  • Identification of 26,850,263 high-confidence SNP.
  • Detection of variation in coding sequences or untranslated regions (UTR) of 78% of porcine genes.
  • Prediction of 1729 loss-of-function variants and identification of 64,232 nonsynonymous variants.
  • Classification of approximately 316,000 SNP as high to moderate impact (loss-of-function, nonsynonymous, or regulatory).

Conclusions:

  • This study significantly enhances the catalog of swine genetic variants, providing a valuable resource for the swine industry.
  • The identified high-impact SNP are key targets for future genome-wide association studies to improve traits.
  • The expanded variant list supports the development of advanced genomic selection strategies in pigs.